This vignette, produced on 2019-08-02, documents the sources of thermodynamic data in CHNOSZ version 1.3.3. All of these data, except for Optional Data, are used in the default database, which is loaded when the package is attached, or by running reset().

The sections below correspond to CSV data files that are stored in the extdata/OBIGT package directory and read by reset() to create the database in the R session (thermo()$obigt). In each section, the primary references (ref1 in thermo()$obigt) are listed in chronological order. Any secondary references (ref2) are listed with bullet points. Each reference is followed by the number of species, and a note (from thermo()$refs). Symbols show whether the data were present in the earliest of the sprons92.dat (ø), slop98.dat (*), slop07.dat (†), or slop16.dat (‡) datafiles for the SUPCRT92 package.

Any additional comments are placed at the beginning of the sections. Abbreviations used below are: Cp (heat capacity), GHS (standard Gibbs energy, enthalpy, entropy), HKF (Helgeson-Kirkham-Flowers equations), V (volume), T (temperature), P (pressure).

Recent changes (2018 - 2019)

Sources of data

Use the tabs below to select a section for viewing. Select “All at once” to show all sections.

Aqueous species

H2O (3)

This file contains H2O, e-, and H+. The properties of H2O are listed as NA; CHNOSZ calculates its properties using a Fortran subroutine taken from SUPRCT92 (Johnson et al., 1992) (default) or using the IAPWS-95 equations (Wagner and Pruß, 2002) or the Deep Earth Water (DEW) model (Sverjensky et al., 2014).

By convention, the standard Gibbs energy of formation, entropy, and heat capacity of the aqueous proton (H+) are 0 at all T and P (e.g. Cox et al., 1989). The formation reaction of the proton can be expressed as ½H2,(g) + Z = H+, where Z is the “element” of positive charge. Because the conventional standard Gibbs energy of this reaction is 0 at all T, the standard entropy of the reaction is also constrained to be zero (cf. Puigdomenech et al., 1997). Therefore, the “element” of positive charge (Z) has zero thermodynamic properties except for an entropy, S°Tr, that is negative one-half that of H2,(g). The standard entropy of the aqueous electron, which is a solely a pseudospecies defined by e- = -Z, is opposite that of Z.**

Despite these considerations, the final column of the thermodynamic database (thermo()$obigt) lists a charge of “0” for both the aqueous proton and electron. Data in this this column are used in CHNOSZ only to specify the charge that is input to the “g-function” (Tanger and Helgeson, 1988; Shock and Helgeson, 1988). Setting it to zero prevents activation of the g-function, which would result in non-zero contributions to thermodynamic properties, conflicting with the conventions mentioned above. All other calculations in CHNOSZ obtain the elemental makeup, including the correct charge for the species, by parsing the chemical formulas stored in the database.^^

**Likewise, GEM-Selektor defines “independent components” to be stoichiometric units usually consisting of elements and charge; the latter, which is named Zz and has a standard molal entropy of -65.34 J/mol/K and heat capacity of -14.418 J/mol/K (negative one-half those of gaseous hydrogen), is negated in the formula of the fictive “aqueous electron” (Kulik, 2006).

^^ Relatedly, charged amino acid sidechain groups have a charge that is tabulated as zero, because other values would be incompatible with group additivity of cations and anions (which have derivatives of the omega parameter (ω) in the revised HKF equations of state that are not opposites of each other) to give a neutral species (for which the derivatives of ω are taken to be zero) (cf. Dick et al., 2006).

Inorganic (837)

Shock and Helgeson (1988) – 57 ionic species (ø)

Shock et al. (1989) – 13 inorganic neutral species (ø)

Shock et al. (1989) – 1 aqueous SiO2 (ø)

Haas et al. (1995) – 249 complexes of rare earth elements (*)

  • slop98.dat – 88 “Corrected values based on data from Haas et al. (1995) (*)

McCollom and Shock (1997) – 2 MgSO4, NaSO4-, and HCl (*)

  • slop98.dat – 2 “Data and parameters as used by McCollom and Shock (1997).” (*)

Shock et al. (1997) – 233 aqueous ions and hydroxide complexes (*)

  • Shock and Helgeson (1988) – 25 values of GHS

  • Sassani and Shock (1998) – 1 Rh+3 (*)

Sverjensky et al. (1997) – 93 metal complexes (*)

  • CHNOSZ – 1 AuCl4- renamed to AuCl4-3

Shock et al. (1997b) – 15 uranium species (*)

Tagirov et al. (1997) – 1 aqueous HCl

Sassani and Shock (1998) – 41 platinum-group ions and complexes (*)

Akinfiev and Zotov (2001) – 15 M+, MCl2-, M(OH)2-, MCl, and MOH (M = Au+, Ag+, or Cu+)

Schulte et al. (2001) – 10 AsH3, CF4, CH3F, Cl2, ClO2, N2O, NF3, NO, PH3, and SF6

Tagirov and Schott (2001) – 17 aqueous Al+3 and complexes

  • Diakonov et al. (1996) – 1 NaAl(OH)4

Nordstrom and Archer (2003) – 10 aqueous As oxides and sulfides

Akinfiev et al. (2006) – 1 AgCl3-2

Accornero et al. (2010) – 43 metal-chromate complexes

Akinfiev and Zotov (2010) – 6 MHS and M(HS)2- (M = Au+, Ag+, or Cu+)

  • Pokrovski et al. (2014) – 1 corrected H of AuHS

Tagirov et al. (2013) – 11 Pd+2 and complexes

Akinfiev and Tagirov (2014) – 13 Zn+2 and complexes

Pokrovski and Dubessy (2015) – 1 trisulfur radical ion

Tagirov et al. (2015) – 5 Pt+2 and complexes

Organic (681)

Shock and Helgeson (1990) – 47 organic species (ø)

  • slop16.dat – 3 hexanol, heptanol, and octanol: “Minor differences in Gibbs energy, entropy, ω, a1, a2, a3, a4 and c1 values compared to Shock and Helgeson (1990).” (‡)

Shock (1993) – 2 ethylacetate and acetamide (*)

Shock and Koretsky (1993) – 104 metal-acetate complexes (*)

  • slop16.dat – 32 “Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements.” (‡)

Shock and McKinnon (1993) – 3 CO, HCN, urea (*)

Schulte and Shock (1993) – 10 aldehydes (*)

  • slop16.dat – 1 formaldehyde: “Entropy corrected to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote i in table 2 of Schulte and Shock (1993).” (‡)

Shock and Koretsky (1995) – 226 metal-organic acid complexes (*)

  • slop98.dat – 6 “These data were used in Shock and Koretsky (1995), but were not tabulated in the paper.” (*)

  • slop16.dat – 55 “Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements.” (‡)

Shock (1995) – 77 carboxylic acids (*)

  • slop16.dat – 2 adipic acid and n-dodecanoate: “Gibbs free energy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements. See footnote y in table 4 of Shock (1995).” (‡)

  • slop16.dat – 1 n-octanoate: “Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements. See footnote ab in table 4 of Shock (1995).” (‡)

Dale et al. (1997) – 10 alkylphenols (*)

Shvedov and Tremaine (1997) – 1 dimethylammonium chloride HKF parameters

Haas and Shock (1999) – 6 chloroethylene species (†)

Prapaipong et al. (1999) – 151 metal-dicarboxylate complexes (†)

  • CHNOSZ – 2 charge of NpO2(Oxal), La(Succ)+, NH4(Succ)-, and NpO2(Succ) as listed by Prapaipong et al. (1999)

Plyasunov and Shock (2001) – 11 aqueous nonelectrolytes (†)

Schulte and Rogers (2004) – 12 alkane thiols (†)

Hawrylak et al. (2006) – 2 methyldiethanolamine and methyldiethanolammonium chloride HKF parameters

Schulte (2010) – 7 organic sulfides

Dick et al. (2013) – 6 phenanthrene and methylphenanthrene isomers

LaRowe and Amend (2019) – 6 dimethylamine, trimethylamine, resorcinol, phloroglucinol, cyclohexane carboxylate, and cyclohexane carboxylic acid

  • Shvedov and Tremaine (1997) – 1 dimethylamine HKF parameters

Biotic (329)

Amend and Helgeson (1997) – 27 amino acids GHS (†)

  • Dick et al. (2006) – 27 amino acids HKF parameters (†)

Amend and Plyasunov (2001) – 10 carbohydrates (†)

  • slop07.dat – 10 high-temperature HKF parameters from Amend and Plyasunov (2001) (†)

LaRowe and Harold C. Helgeson (2006a) – 138 nucleic-acid bases, nucleosides, and nucleotides (†)

  • Lowe et al. (2017) – 1 adenine HKF parameters

LaRowe and Harold C. Helgeson (2006a) – 4 citric acid and citrate

  • Canovas and Shock (2016) – 4 citric acid species HKF a1–a4 parameters

LaRowe and Harold C. Helgeson (2006b) – 32 Mg-complexed adenosine nucleotides (ATP), NAD, and NADP (†)

Dick et al. (2006) – 38 amino acid, protein, and organic groups

  • LaRowe and Dick (2012) – 1 methionine sidechain GHS

  • CHNOSZ – 1 Incorrect values of HKF a1–a4 parameters for [-CH2NH2] were printed in Table 6 of Dick et al. (2006); corrected values are used here.

Dick et al. (2006) – 19 Gly-X-Gly tripeptides Cp, V, and HKF c1, c2, ω parameters

Dick (2007) – 4 glutathione, cystine, and cystine sidechain

LaRowe and Dick (2012) – 1 methionine GHS

  • Dick et al. (2006) – 1 methionine HKF parameters (†)

Kitadai (2014) – 12 glycine, diglycine, and triglycine (zwitterions and ions); diketopiperazine, [Gly] and [UPBB] groups

  • Shock (1992) – 1 diketopiperazine GHS

  • Goldberg et al. (2002) – 6 glycine, diglycine, and triglycine (+1 and -1 ions) GHS

  • Dick et al. (2006) – 3 glycine, [Gly], and [UPBB] HKF parameters

  • Dick et al. (2006) – 1 triglycine Cp, V, and HKF c1, c2, ω parameters

Canovas and Shock (2016) – 22 citric acid cycle metabolites

Azadi et al. (2019) – 22 metal-glycinate complexes

  • CHNOSZ – 20 recalculated values of Cp (those in Azadi et al. (2019) appear to be calculated using wrong sign on ω) and enthalpy (using ΔG=ΔH-TΔS and the entropies of the elements)

  • CHNOSZ – 2 Tl(Gly) and Tl(Gly)2-: change Ti to Tl

Solids

Inorganic (134)

Chamosite,7A and witherite were present in sprons92.dat but not in slop98.dat or later files, and are not included in CHNOSZ.

The source of parameters used here for goethite is different from that in the slop files (Shock, 2009).

Helgeson et al. (1978) – 56 data for minerals and phase transitions (ø)

  • Pankratz and King (1970) – 2 bornite and chalcopyrite (ø)

  • Wagman et al. (1982) – 1 manganosite (ø)

  • Helgeson (1985) – 1 ferrosilite and siderite (ø)

  • CHNOSZ – 15 GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.

Robie et al. (1978) – 1 chlorargyrite (ø)

  • Pankratz (1970) – 1 chlorargyrite (ø)

Robie et al. (1978) – 4 iron (ø)

  • Kelley (1960) – 1 iron Cp (ø)

  • CHNOSZ – 3 GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.

Robie et al. (1978) – 1 gibbsite GHS

  • Zimmer et al. (2016) – 1 Cp parameters listed in spronsbl.dat

Wagman et al. (1982) – 1 MgSO4

Jackson and Helgeson (1985) – 5 Sn minerals (ø)

  • CHNOSZ – 1 GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.

Reardon and Armstrong (1987) – 1 celestite GHS

  • Helgeson et al. (1978) – 1 celestite V and Cp parameters (ø)

Ball and Nordstrom (1991) – 1 arsenopyrite: G

  • Zimmer et al. (2016) – 1 data listed in spronsbl.dat

Hemingway et al. (1991) – 1 boehmite

  • Zimmer et al. (2016) – 1 Cp parameters listed in spronsbl.dat

Parker and Khodakovskii (1995) – 1 melanterite

Robie and Hemingway (1995) – 1 gypsum GHS

  • Kelley (1960) – 1 gypsum Cp

McCollom and Shock (1997) – 3 sulfur (*)

  • slop98.dat – 3 “Data and parameters as used by McCollom and Shock (1997).” (*)

Shock et al. (1997) – 2 zincite and litharge (*)

  • Helgeson et al. (1978) – 1 litharge S, V, and Cp parameters (ø)

  • slop98.dat – 1 zincite and litharge; “These data were used in Shock et al. (1997), but were not tabulated in the paper.” (*)

Shock et al. (1997b) – 1 uraninite (*)

Sassani and Shock (1998) – 15 platinum-group solids (*)

Stoffregen et al. (2000) – 3 jarosite, natroalunite, and natrojarosite

Wood and Samson (2000) – 2 scheelite and ferberite; adopted values include Cp parameters for scheelite from Barin and Knacke (1973) and GHS and Cp parameters for ferberite from Polya (1990)

  • Robie et al. (1978) – 1 scheelite GHS and V

  • Robie et al. (1978) – 1 ferberite V

Amend and Shock (2001) – 3 selenium and molybdenite (†)

Mercury et al. (2001) – 8 polymorphs of ice

Juraj Majzlan, Grevel, et al. (2003) – 3 goethite, lepidocrocite, and maghemite GHS

  • Juraj Majzlan, Lang, et al. (2003) – 3 goethite, lepidocrocite, and maghemite Cp

Nordstrom and Archer (2003) – 8 As oxide and sulfide minerals

  • Zimmer et al. (2016) – 1 As(α): V listed in spronsbl.dat

Majzlan et al. (2004) – 1 hydronium jarosite

Zhu et al. (2005) – 2 barium arsenate and barium hydrogen arsenate: G

  • Zimmer et al. (2016) – 2 data listed in spronsbl.dat

Langmuir et al. (2006) – 2 scorodite and amorphous ferric arsenate: G

  • Zimmer et al. (2016) – 2 data listed in spronsbl.dat

Majzlan et al. (2006) – 3 coquimbite, ferricopiapite, and rhomboclase

Grevel and Majzlan (2009) – 4 kieserite, starkeyite, hexahydrite, and epsomite

Zimmer et al. (2016) – 1 dawsonite GHS

  • Robie and Hemingway (1995) – 1 dawsonite: Cp coefficients corrected in Tutolo et al. (2014); Cp value at 25 °C from Bénézeth et al. (2007), citing Ferrante et al. (1976)

Organic (479)

Tardy et al. (1997) – 5 humic acid, microflora, and plants

Helgeson et al. (1998) – 59 organic molecules and groups

Helgeson et al. (1998) – 20 amino acids

  • LaRowe and Dick (2012) – 4 updated and corrected parameters for cysteine, glycine, leucine, and methionine

Richard and Helgeson (1998) – 311 organic molecules and groups

Richard (2001) – 8 organic sulfur compounds

LaRowe and Harold C. Helgeson (2006a) – 19 nucleic-acid bases, nucleosides, and nucleotides

LaRowe and Harold C. Helgeson (2006b) – 9 Mg-complexed adenosine nucleotides (ATP), NAD, and NADP

Helgeson et al. (2009) – 5 kerogens

Richard and Gaona (2011) – 13 organic iodine compounds

LaRowe and Dick (2012) – 30 4-hydroxyproline, 5-hydroxylysine, 4 dipeptides, and sidechain and backbone groups in proteins

Berman (92)

This file gives the identifiying information for minerals whose properties are calculated using the formulation of Berman (1988). Note that thermodynamic properties for these minerals are listed as NA in thermo()$obigt; the actual data are stored separately, as CSV files in extdata/Berman/*.csv.

Berman (1988) – 65 minerals

  • Berman (1990) – 2 almandine and ilmenite: modified H and/or S

  • Sverjensky et al. (1991) – 9 G and H revisions for K- and Al-bearing silicates

  • Sverjensky et al. (1991) – 1 phlogopite: H and S modified by Berman (1990), followed by G and H revision for K-bearing silicates (after Sverjensky et al., 1991)

  • berman.dat (2017) – 1 antigorite: “Oct. 21, 2016: Revised volume coefficients consistent with Hilairet et al. (2006) and Yang et al. (2014)

Berman (1990) – 1 annite

  • Sverjensky et al. (1991) – 1 annite: G and H revision for K-bearing silicates (after Sverjensky et al., 1991)

Evans (1990) – 2 glaucophane and pumpellyite

  • JUN92.bs (1992) – 2 data as listed in JUN92.bs data file

Vidal et al. (1992) – 1 sudoite

Zhu and Sverjensky (1992) – 10 F,Cl,OH biotite and apatite endmembers. GHS and V were taken from Table 6 of Zhu and Sverjensky (1992); heat capacity and volume parameters from berman.dat.

Vidal et al. (2001) – 2 daphnite and Mg-amesite

Gottschalk (2004) – 4 zoisite, clinozoisite, and epidote

Vidal et al. (2005) – 1 Fe-amesite

Delgado Martín and Soler i Gil (2010) – 5 hedenbergite, andradite, ferro-actinolite, grunerite, and ilvaite

Facq et al. (2014) – 1 aragonite; source of data: berman.dat

Liquids

Organic (532)

Helgeson et al. (1998) – 186 organic molecules and groups

Richard and Helgeson (1998) – 231 organic molecules and groups

Richard (2001) – 67 organic sulfur compounds

LaRowe and Harold C. Helgeson (2006b) – 2 pyridine and piperidine

Richard (2008) – 17 alkenes

Richard and Gaona (2011) – 29 organic iodine compounds

Gases

Inorganic (19)

Wagman et al. (1982) – 2 gases GHS (†)

  • Amend and Shock (2001) – 2 NO and N2O (†)

Wagman et al. (1982) – 15 gases GHS (ø)

  • Kelley (1960) – 15 gases Cp (ø)

Robie and Hemingway (1995) – 2 hydrogen fluoride and hydrogen chloride

Organic (266)

Shock (1993) – 2 carbon monoxide and ethylene (*)

Dale et al. (1997) – 4 phenol, and cresol isomers (*)

Dale et al. (1997) – 6 dimethylphenol isomers

Helgeson et al. (1998) – 153 organic molecules and groups

Richard (2001) – 62 organic sulfur compounds

Richard and Gaona (2011) – 39 organic iodine compounds

Optional Data

DEW (199)

The Deep Earth Water (DEW) model extends the applicability of the revised HKF equations of state to 60 kbar. Accuracy of the thermodynamic calculations at these conditions is improved by revised correlations for the a1 HKF parameter, as described by Sverjensky et al., 2014. The data here were taken from the May 2017 version of the DEW spreadsheet (Dew Model, 2017). The following species are present in the spreadsheet, but are not used here because the parameters are unchanged from the default database in CHNOSZ: B(OH)3, Br-, Ca+2, Cl-, Cs+, F-, H+, H2, He, I-, K+, Kr, Li+, Mg+2, Na+, Ne, O2, Rb+, Rn.

Besides using add.obigt('DEW') to load these data, you should also run water('DEW') to activate the DEW equations in CHNOSZ. See demo(DEW) for some examples.

Shock and Helgeson (1988) – 2 ionic species

  • Sverjensky et al. (2014) – 2 revisions for BO(OH) and BO2-

Shock and Helgeson (1990) – 3 formic acid, formate, and propanoate

  • DEW model (2017) – 1 revised with new predicted a1 for ions

  • DEW model (2017) – 1 revised with new predicted a1 for complex species

  • DEW model (2017) – 1 propanoate: Revised a1 from new delVn correlation for -1 ions

Pokrovskii and Helgeson (1995) – 2 aluminum species

  • Sverjensky et al. (2014) – 2 revisions for AlO2- and HAlO2

Ho and Palmer (1997) – 1 KOH

  • Sverjensky et al. (2014) – 1 Fitted to Ho and Palmer (1997) data with a1 pred. from the sum of the ions and used to predict the volume

Plyasunov and Shock (2001) – 2 acetic acid, propanoic acid, and methane

  • DEW model (2017) – 1 methane: revised with new predicted a1 for complex species

Facq et al. (2014) – 3 CO2, CO3-2, and HCO3-

Sverjensky et al. (2014) – 2 SiO2 and Si2O4

DEW model (2017) – 184 other data from Aqueous Species Table in spreadsheet (see detailed references there)

  • DEW model (2017) – 1 acetate: revised January 26th, 2016; new a1 value from complexes and organics correlation.

  • DEW model (2017) – 1 MgCl+: revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions

  • DEW model (2017) – 1 NaCl: revised with new predicted a1 for complex species

SUPCRT92 (180)

These minerals and aqueous species, taken from the SUPCRT92 database, were present in earlier versions of CHNOSZ but have since been superseded by Berman (1988) (minerals) and Nordstrom and Archer (2003) (H2AsO3-). The thermodynamic properties and parameters are kept here as optional data for reproducing published calculations and making comparisons with newer data. The minerals here include all of the silicates and Al-bearing minerals from Helgeson et al. (1978), as well as calcite, dolomite, hematite, and magnetite. Use add.obigt("SUPCRT92") to load the data. NOTE: Other minerals from SUPCRT92, including native elements, sulfides, halides, sulfates, and selected carbonates and oxides that do not duplicate those in the Berman dataset, are still present in the default database (inorganic_cr.csv).

Helgeson et al. (1978) – 178 data for minerals and phase transitions (ø)

  • Kelley (1960) – 1 larnite Cp (ø)

  • Robie et al. (1978) – 4 dickite, fluorphlogopite, halloysite, and pyrope (ø)

  • Plummer and Busenberg (1982) – 2 aragonite and calcite (ø)

  • Helgeson (1985) – 1 ferrosilite and siderite (ø)

  • sprons92.dat – 24 Ca-bearing minerals; “Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca2+ and CO32- (Shock and Helgeson, 1988) together with the solubilities of calcite and aragonite reported by Plummer and Busenberg (1982) (ø)

  • slop98.dat – 1 daphnite; “Gf and Hf from Saccocia and Seyfried (1993) TMM” (*)

  • CHNOSZ – 53 GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.

Robie et al. (1978) – 2 rutile and titanite (ø)

  • Bowers and Helgeson (1983) – 1 rutile (ø)

  • sprons92.dat – 1 titanite: Bowers and Helgeson (1983) + “Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca2+ and CO32- (Shock and Helgeson, 1988) together with the solubilities of calcite and aragonite reported by Plummer and Busenberg (1982) (ø)

SLOP98 (169)

These species, which were taken from or are linked to slop98.dat (or later versions) and were present in earlier versions of CHNOSZ, have been replaced by or are incompatible with species currently in the default database, including aqueous Al species (Tagirov and Schott, 2001), As species (Nordstrom and Archer, 2003), Au, Ag, and Cu species (Akinfiev and Zotov, 2001; Akinfiev and Zotov, 2010), Pd species (Tagirov et al., 2013), Zn species (Akinfiev and Tagirov, 2014), and Pt species (Tagirov et al., 2015). This file also contains aqueous transuranic actinide complexes, for which estimated thermodynamic properties have been reported, but no entropies of the corresponding elements at 298.15 K are available to check the self-consistency of the GHS values for the complexes. Use add.obigt("SLOP98") to load the data. NOTE: Many other species found in slop98.dat and later versions are still present in the default database.

Shock and Helgeson (1988) – 1 H2AsO3- (ø)

Shock and Helgeson (1988) – 1 Ag+ (ø)

Shock and Koretsky (1993) – 9 Ag-, Au-, Cu(I)- and Al-acetate complexes (*)

McCollom and Shock (1997) – 1 aqueous HCl (*)

  • slop98.dat – 1 “Data and parameters as used by McCollom and Shock (1997).” (*)

Shock et al. (1997) – 1 aqueous ions and hydroxide complexes (*)

Shock et al. (1997) – 2 Au+ and Cu+ (*)

  • Shock and Helgeson (1988) – 2 values of GHS

Shock et al. (1997) – 6 arsenate and arsenite species (*)

Shock et al. (1997) – 5 Al+3 and Al-hydroxide complexes (*)

Shock et al. (1997) – 5 Zn+2 and Zn-hydroxide complexes (*)

  • Shock and Helgeson (1988) – 1 values of GHS

Sverjensky et al. (1997) – 2 Au(HS)2- and Ag(HS)2- (*)

Sverjensky et al. (1997) – 10 Au-, Ag-, Cu- and Zn-chloride complexes (*)

Sverjensky et al. (1997) – 3 Zn-acetate complexes (*)

  • slop16.dat – 1 Zn(Ac)3-: “Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote h in table 2 of Sverjensky et al. (1997).” (‡)

Sassani and Shock (1998) – 20 Pd+2 and Pt+2 and their complexes (*)

Murphy and Shock (1999) – 38 actinides (†)

Prapaipong et al. (1999) – 9 metal-dicarboxylate complexes (†)

  • slop07.dat – 1 corrected charge of Pu(Oxal)+2 (†)

  • CHNOSZ – 2 charge of NpO2(Oxal), La(Succ)+, NH4(Succ)-, and NpO2(Succ) as listed by Prapaipong et al. (1999)

Prapaipong et al. (1999) – 2 Al(Mal)+ and Al(Oxal)+ (†)

Marini and Accornero (2007) – 52 metal-arsenate and metal-arsenite complexes; linked to properties of arsenate and arsenite from Shock et al. (1997)

  • Marini and Accornero (2010) – 52 corrected values

Accornero et al. (2010) – 2 Np- and Am-chromate complexes

OldAA (64)

Data for these amino acids and related species were present in earlier versions of CHNOSZ but have been replaced by or are incompatible with later updates (LaRowe and Dick, 2012; Kitadai, 2014; Azadi et al., 2019). Use add.obigt("OldAA") to load the data.

Shock (1992) – 4 diglycine, alanylglycine, leucylglycine, and diketopiperazine; not present in slop files after slop98.dat (*)

Shock and Koretsky (1995) – 54 alanate, glycinate and their complexes with metals. Values are taken from slop98.dat, which notes corrected values for some species. (*)

  • Amend and Helgeson (1997) – 2 alanate and glycinate GHS

  • CHNOSZ – 52 metal-amino acid complexes: GHS were recalculated by adding the differences between values from Shock and Koretsky (1995) and Amend and Helgeson (1997) for alanate or glycinate to the properties of the complexes reported by Shock and Koretsky (1995).

Amend and Helgeson (1997) – 3 glycine, glycinium, and methionine GHS

  • Dick et al. (2006) – 3 amino acids HKF parameters

Dick et al. (2006) – 3 [Gly], [Met], and [UPBB]

AS04 (3)

This file has data for aqueous SiO2 from Apps and Spycher (2004) and a modified HSiO3- to be consistent with the SiO2 here. This file also has H4SiO4 from an earlier publication (Stefánsson, 2001) that is roughly consistent with SiO2 here (see ?add.obigt). Use add.obigt("AS04") to load the data; see Regressing thermodynamic data for an example.

Sverjensky et al. (1997) – 1 HSiO3- (*)

  • CHNOSZ – 1 GHS recalculated by adding difference from SiO2 (Sverjensky et al., 1997) to updated values for SiO2 (Apps and Spycher, 2004)

Stefánsson (2001) – 1 aqueous H4SiO4

Apps and Spycher (2004) – 1 aqueous SiO2

AkDi (24)

This file has parameters for aqueous nonelectrolytes in the Akinfiev-Diamond model (Akinfiev and Diamond, 2003). Use add.obigt("AkDi") to load the data; see demo(AkDi) for an example.

Akinfiev and Diamond (2003) – 10 dissolved gas species; parameters estimated from the experimental Henry’s constant

Akinfiev and Diamond (2003) – 8 dissolved gas species; parameters estimated from standard-state properties at 25 ° C

Akinfiev and Plyasunov (2014) – 6 B(OH)3, Si(OH)4, and As(OH)3

All at once

Aqueous species

H2O (3)

This file contains H2O, e-, and H+. The properties of H2O are listed as NA; CHNOSZ calculates its properties using a Fortran subroutine taken from SUPRCT92 (Johnson et al., 1992) (default) or using the IAPWS-95 equations (Wagner and Pruß, 2002) or the Deep Earth Water (DEW) model (Sverjensky et al., 2014).

By convention, the standard Gibbs energy of formation, entropy, and heat capacity of the aqueous proton (H+) are 0 at all T and P (e.g. Cox et al., 1989). The formation reaction of the proton can be expressed as ½H2,(g) + Z = H+, where Z is the “element” of positive charge. Because the conventional standard Gibbs energy of this reaction is 0 at all T, the standard entropy of the reaction is also constrained to be zero (cf. Puigdomenech et al., 1997). Therefore, the “element” of positive charge (Z) has zero thermodynamic properties except for an entropy, S°Tr, that is negative one-half that of H2,(g). The standard entropy of the aqueous electron, which is a solely a pseudospecies defined by e- = -Z, is opposite that of Z.**

Despite these considerations, the final column of the thermodynamic database (thermo()$obigt) lists a charge of “0” for both the aqueous proton and electron. Data in this this column are used in CHNOSZ only to specify the charge that is input to the “g-function” (Tanger and Helgeson, 1988; Shock and Helgeson, 1988). Setting it to zero prevents activation of the g-function, which would result in non-zero contributions to thermodynamic properties, conflicting with the conventions mentioned above. All other calculations in CHNOSZ obtain the elemental makeup, including the correct charge for the species, by parsing the chemical formulas stored in the database.^^

**Likewise, GEM-Selektor defines “independent components” to be stoichiometric units usually consisting of elements and charge; the latter, which is named Zz and has a standard molal entropy of -65.34 J/mol/K and heat capacity of -14.418 J/mol/K (negative one-half those of gaseous hydrogen), is negated in the formula of the fictive “aqueous electron” (Kulik, 2006).

^^ Relatedly, charged amino acid sidechain groups have a charge that is tabulated as zero, because other values would be incompatible with group additivity of cations and anions (which have derivatives of the omega parameter (ω) in the revised HKF equations of state that are not opposites of each other) to give a neutral species (for which the derivatives of ω are taken to be zero) (cf. Dick et al., 2006).

Inorganic (837)

Shock and Helgeson (1988) – 57 ionic species (ø)

Shock et al. (1989) – 13 inorganic neutral species (ø)

Shock et al. (1989) – 1 aqueous SiO2 (ø)

Haas et al. (1995) – 249 complexes of rare earth elements (*)

  • slop98.dat – 88 “Corrected values based on data from Haas et al. (1995) (*)

McCollom and Shock (1997) – 2 MgSO4, NaSO4-, and HCl (*)

  • slop98.dat – 2 “Data and parameters as used by McCollom and Shock (1997).” (*)

Shock et al. (1997) – 233 aqueous ions and hydroxide complexes (*)

  • Shock and Helgeson (1988) – 25 values of GHS

  • Sassani and Shock (1998) – 1 Rh+3 (*)

Sverjensky et al. (1997) – 93 metal complexes (*)

  • CHNOSZ – 1 AuCl4- renamed to AuCl4-3

Shock et al. (1997b) – 15 uranium species (*)

Tagirov et al. (1997) – 1 aqueous HCl

Sassani and Shock (1998) – 41 platinum-group ions and complexes (*)

Akinfiev and Zotov (2001) – 15 M+, MCl2-, M(OH)2-, MCl, and MOH (M = Au+, Ag+, or Cu+)

Schulte et al. (2001) – 10 AsH3, CF4, CH3F, Cl2, ClO2, N2O, NF3, NO, PH3, and SF6

Tagirov and Schott (2001) – 17 aqueous Al+3 and complexes

  • Diakonov et al. (1996) – 1 NaAl(OH)4

Nordstrom and Archer (2003) – 10 aqueous As oxides and sulfides

Akinfiev et al. (2006) – 1 AgCl3-2

Accornero et al. (2010) – 43 metal-chromate complexes

Akinfiev and Zotov (2010) – 6 MHS and M(HS)2- (M = Au+, Ag+, or Cu+)

  • Pokrovski et al. (2014) – 1 corrected H of AuHS

Tagirov et al. (2013) – 11 Pd+2 and complexes

Akinfiev and Tagirov (2014) – 13 Zn+2 and complexes

Pokrovski and Dubessy (2015) – 1 trisulfur radical ion

Tagirov et al. (2015) – 5 Pt+2 and complexes

Organic (681)

Shock and Helgeson (1990) – 47 organic species (ø)

  • slop16.dat – 3 hexanol, heptanol, and octanol: “Minor differences in Gibbs energy, entropy, ω, a1, a2, a3, a4 and c1 values compared to Shock and Helgeson (1990).” (‡)

Shock (1993) – 2 ethylacetate and acetamide (*)

Shock and Koretsky (1993) – 104 metal-acetate complexes (*)

  • slop16.dat – 32 “Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements.” (‡)

Shock and McKinnon (1993) – 3 CO, HCN, urea (*)

Schulte and Shock (1993) – 10 aldehydes (*)

  • slop16.dat – 1 formaldehyde: “Entropy corrected to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote i in table 2 of Schulte and Shock (1993).” (‡)

Shock and Koretsky (1995) – 226 metal-organic acid complexes (*)

  • slop98.dat – 6 “These data were used in Shock and Koretsky (1995), but were not tabulated in the paper.” (*)

  • slop16.dat – 55 “Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements.” (‡)

Shock (1995) – 77 carboxylic acids (*)

  • slop16.dat – 2 adipic acid and n-dodecanoate: “Gibbs free energy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements. See footnote y in table 4 of Shock (1995).” (‡)

  • slop16.dat – 1 n-octanoate: “Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements. See footnote ab in table 4 of Shock (1995).” (‡)

Dale et al. (1997) – 10 alkylphenols (*)

Shvedov and Tremaine (1997) – 1 dimethylammonium chloride HKF parameters

Haas and Shock (1999) – 6 chloroethylene species (†)

Prapaipong et al. (1999) – 151 metal-dicarboxylate complexes (†)

  • CHNOSZ – 2 charge of NpO2(Oxal), La(Succ)+, NH4(Succ)-, and NpO2(Succ) as listed by Prapaipong et al. (1999)

Plyasunov and Shock (2001) – 11 aqueous nonelectrolytes (†)

Schulte and Rogers (2004) – 12 alkane thiols (†)

Hawrylak et al. (2006) – 2 methyldiethanolamine and methyldiethanolammonium chloride HKF parameters

Schulte (2010) – 7 organic sulfides

Dick et al. (2013) – 6 phenanthrene and methylphenanthrene isomers

LaRowe and Amend (2019) – 6 dimethylamine, trimethylamine, resorcinol, phloroglucinol, cyclohexane carboxylate, and cyclohexane carboxylic acid

  • Shvedov and Tremaine (1997) – 1 dimethylamine HKF parameters

Biotic (329)

Amend and Helgeson (1997) – 27 amino acids GHS (†)

  • Dick et al. (2006) – 27 amino acids HKF parameters (†)

Amend and Plyasunov (2001) – 10 carbohydrates (†)

  • slop07.dat – 10 high-temperature HKF parameters from Amend and Plyasunov (2001) (†)

LaRowe and Harold C. Helgeson (2006a) – 138 nucleic-acid bases, nucleosides, and nucleotides (†)

  • Lowe et al. (2017) – 1 adenine HKF parameters

LaRowe and Harold C. Helgeson (2006a) – 4 citric acid and citrate

  • Canovas and Shock (2016) – 4 citric acid species HKF a1–a4 parameters

LaRowe and Harold C. Helgeson (2006b) – 32 Mg-complexed adenosine nucleotides (ATP), NAD, and NADP (†)

Dick et al. (2006) – 38 amino acid, protein, and organic groups

  • LaRowe and Dick (2012) – 1 methionine sidechain GHS

  • CHNOSZ – 1 Incorrect values of HKF a1–a4 parameters for [-CH2NH2] were printed in Table 6 of Dick et al. (2006); corrected values are used here.

Dick et al. (2006) – 19 Gly-X-Gly tripeptides Cp, V, and HKF c1, c2, ω parameters

Dick (2007) – 4 glutathione, cystine, and cystine sidechain

LaRowe and Dick (2012) – 1 methionine GHS

  • Dick et al. (2006) – 1 methionine HKF parameters (†)

Kitadai (2014) – 12 glycine, diglycine, and triglycine (zwitterions and ions); diketopiperazine, [Gly] and [UPBB] groups

  • Shock (1992) – 1 diketopiperazine GHS

  • Goldberg et al. (2002) – 6 glycine, diglycine, and triglycine (+1 and -1 ions) GHS

  • Dick et al. (2006) – 3 glycine, [Gly], and [UPBB] HKF parameters

  • Dick et al. (2006) – 1 triglycine Cp, V, and HKF c1, c2, ω parameters

Canovas and Shock (2016) – 22 citric acid cycle metabolites

Azadi et al. (2019) – 22 metal-glycinate complexes

  • CHNOSZ – 20 recalculated values of Cp (those in Azadi et al. (2019) appear to be calculated using wrong sign on ω) and enthalpy (using ΔG=ΔH-TΔS and the entropies of the elements)

  • CHNOSZ – 2 Tl(Gly) and Tl(Gly)2-: change Ti to Tl

Solids

Inorganic (134)

Chamosite,7A and witherite were present in sprons92.dat but not in slop98.dat or later files, and are not included in CHNOSZ.

The source of parameters used here for goethite is different from that in the slop files (Shock, 2009).

Helgeson et al. (1978) – 56 data for minerals and phase transitions (ø)

  • Pankratz and King (1970) – 2 bornite and chalcopyrite (ø)

  • Wagman et al. (1982) – 1 manganosite (ø)

  • Helgeson (1985) – 1 ferrosilite and siderite (ø)

  • CHNOSZ – 15 GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.

Robie et al. (1978) – 1 chlorargyrite (ø)

  • Pankratz (1970) – 1 chlorargyrite (ø)

Robie et al. (1978) – 4 iron (ø)

  • Kelley (1960) – 1 iron Cp (ø)

  • CHNOSZ – 3 GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.

Robie et al. (1978) – 1 gibbsite GHS

  • Zimmer et al. (2016) – 1 Cp parameters listed in spronsbl.dat

Wagman et al. (1982) – 1 MgSO4

Jackson and Helgeson (1985) – 5 Sn minerals (ø)

  • CHNOSZ – 1 GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.

Reardon and Armstrong (1987) – 1 celestite GHS

  • Helgeson et al. (1978) – 1 celestite V and Cp parameters (ø)

Ball and Nordstrom (1991) – 1 arsenopyrite: G

  • Zimmer et al. (2016) – 1 data listed in spronsbl.dat

Hemingway et al. (1991) – 1 boehmite

  • Zimmer et al. (2016) – 1 Cp parameters listed in spronsbl.dat

Parker and Khodakovskii (1995) – 1 melanterite

Robie and Hemingway (1995) – 1 gypsum GHS

  • Kelley (1960) – 1 gypsum Cp

McCollom and Shock (1997) – 3 sulfur (*)

  • slop98.dat – 3 “Data and parameters as used by McCollom and Shock (1997).” (*)

Shock et al. (1997) – 2 zincite and litharge (*)

  • Helgeson et al. (1978) – 1 litharge S, V, and Cp parameters (ø)

  • slop98.dat – 1 zincite and litharge; “These data were used in Shock et al. (1997), but were not tabulated in the paper.” (*)

Shock et al. (1997b) – 1 uraninite (*)

Sassani and Shock (1998) – 15 platinum-group solids (*)

Stoffregen et al. (2000) – 3 jarosite, natroalunite, and natrojarosite

Wood and Samson (2000) – 2 scheelite and ferberite; adopted values include Cp parameters for scheelite from Barin and Knacke (1973) and GHS and Cp parameters for ferberite from Polya (1990)

  • Robie et al. (1978) – 1 scheelite GHS and V

  • Robie et al. (1978) – 1 ferberite V

Amend and Shock (2001) – 3 selenium and molybdenite (†)

Mercury et al. (2001) – 8 polymorphs of ice

Juraj Majzlan, Grevel, et al. (2003) – 3 goethite, lepidocrocite, and maghemite GHS

  • Juraj Majzlan, Lang, et al. (2003) – 3 goethite, lepidocrocite, and maghemite Cp

Nordstrom and Archer (2003) – 8 As oxide and sulfide minerals

  • Zimmer et al. (2016) – 1 As(α): V listed in spronsbl.dat

Majzlan et al. (2004) – 1 hydronium jarosite

Zhu et al. (2005) – 2 barium arsenate and barium hydrogen arsenate: G

  • Zimmer et al. (2016) – 2 data listed in spronsbl.dat

Langmuir et al. (2006) – 2 scorodite and amorphous ferric arsenate: G

  • Zimmer et al. (2016) – 2 data listed in spronsbl.dat

Majzlan et al. (2006) – 3 coquimbite, ferricopiapite, and rhomboclase

Grevel and Majzlan (2009) – 4 kieserite, starkeyite, hexahydrite, and epsomite

Zimmer et al. (2016) – 1 dawsonite GHS

  • Robie and Hemingway (1995) – 1 dawsonite: Cp coefficients corrected in Tutolo et al. (2014); Cp value at 25 °C from Bénézeth et al. (2007), citing Ferrante et al. (1976)

Organic (479)

Tardy et al. (1997) – 5 humic acid, microflora, and plants

Helgeson et al. (1998) – 59 organic molecules and groups

Helgeson et al. (1998) – 20 amino acids

  • LaRowe and Dick (2012) – 4 updated and corrected parameters for cysteine, glycine, leucine, and methionine

Richard and Helgeson (1998) – 311 organic molecules and groups

Richard (2001) – 8 organic sulfur compounds

LaRowe and Harold C. Helgeson (2006a) – 19 nucleic-acid bases, nucleosides, and nucleotides

LaRowe and Harold C. Helgeson (2006b) – 9 Mg-complexed adenosine nucleotides (ATP), NAD, and NADP

Helgeson et al. (2009) – 5 kerogens

Richard and Gaona (2011) – 13 organic iodine compounds

LaRowe and Dick (2012) – 30 4-hydroxyproline, 5-hydroxylysine, 4 dipeptides, and sidechain and backbone groups in proteins

Berman (92)

This file gives the identifiying information for minerals whose properties are calculated using the formulation of Berman (1988). Note that thermodynamic properties for these minerals are listed as NA in thermo()$obigt; the actual data are stored separately, as CSV files in extdata/Berman/*.csv.

Berman (1988) – 65 minerals

  • Berman (1990) – 2 almandine and ilmenite: modified H and/or S

  • Sverjensky et al. (1991) – 9 G and H revisions for K- and Al-bearing silicates

  • Sverjensky et al. (1991) – 1 phlogopite: H and S modified by Berman (1990), followed by G and H revision for K-bearing silicates (after Sverjensky et al., 1991)

  • berman.dat (2017) – 1 antigorite: “Oct. 21, 2016: Revised volume coefficients consistent with Hilairet et al. (2006) and Yang et al. (2014)

Berman (1990) – 1 annite

  • Sverjensky et al. (1991) – 1 annite: G and H revision for K-bearing silicates (after Sverjensky et al., 1991)

Evans (1990) – 2 glaucophane and pumpellyite

  • JUN92.bs (1992) – 2 data as listed in JUN92.bs data file

Vidal et al. (1992) – 1 sudoite

Zhu and Sverjensky (1992) – 10 F,Cl,OH biotite and apatite endmembers. GHS and V were taken from Table 6 of Zhu and Sverjensky (1992); heat capacity and volume parameters from berman.dat.

Vidal et al. (2001) – 2 daphnite and Mg-amesite

Gottschalk (2004) – 4 zoisite, clinozoisite, and epidote

Vidal et al. (2005) – 1 Fe-amesite

Delgado Martín and Soler i Gil (2010) – 5 hedenbergite, andradite, ferro-actinolite, grunerite, and ilvaite

Facq et al. (2014) – 1 aragonite; source of data: berman.dat

Liquids

Organic (532)

Helgeson et al. (1998) – 186 organic molecules and groups

Richard and Helgeson (1998) – 231 organic molecules and groups

Richard (2001) – 67 organic sulfur compounds

LaRowe and Harold C. Helgeson (2006b) – 2 pyridine and piperidine

Richard (2008) – 17 alkenes

Richard and Gaona (2011) – 29 organic iodine compounds

Gases

Inorganic (19)

Wagman et al. (1982) – 2 gases GHS (†)

  • Amend and Shock (2001) – 2 NO and N2O (†)

Wagman et al. (1982) – 15 gases GHS (ø)

  • Kelley (1960) – 15 gases Cp (ø)

Robie and Hemingway (1995) – 2 hydrogen fluoride and hydrogen chloride

Organic (266)

Shock (1993) – 2 carbon monoxide and ethylene (*)

Dale et al. (1997) – 4 phenol, and cresol isomers (*)

Dale et al. (1997) – 6 dimethylphenol isomers

Helgeson et al. (1998) – 153 organic molecules and groups

Richard (2001) – 62 organic sulfur compounds

Richard and Gaona (2011) – 39 organic iodine compounds

Optional Data

DEW (199)

The Deep Earth Water (DEW) model extends the applicability of the revised HKF equations of state to 60 kbar. Accuracy of the thermodynamic calculations at these conditions is improved by revised correlations for the a1 HKF parameter, as described by Sverjensky et al., 2014. The data here were taken from the May 2017 version of the DEW spreadsheet (Dew Model, 2017). The following species are present in the spreadsheet, but are not used here because the parameters are unchanged from the default database in CHNOSZ: B(OH)3, Br-, Ca+2, Cl-, Cs+, F-, H+, H2, He, I-, K+, Kr, Li+, Mg+2, Na+, Ne, O2, Rb+, Rn.

Besides using add.obigt('DEW') to load these data, you should also run water('DEW') to activate the DEW equations in CHNOSZ. See demo(DEW) for some examples.

Shock and Helgeson (1988) – 2 ionic species

  • Sverjensky et al. (2014) – 2 revisions for BO(OH) and BO2-

Shock and Helgeson (1990) – 3 formic acid, formate, and propanoate

  • DEW model (2017) – 1 revised with new predicted a1 for ions

  • DEW model (2017) – 1 revised with new predicted a1 for complex species

  • DEW model (2017) – 1 propanoate: Revised a1 from new delVn correlation for -1 ions

Pokrovskii and Helgeson (1995) – 2 aluminum species

  • Sverjensky et al. (2014) – 2 revisions for AlO2- and HAlO2

Ho and Palmer (1997) – 1 KOH

  • Sverjensky et al. (2014) – 1 Fitted to Ho and Palmer (1997) data with a1 pred. from the sum of the ions and used to predict the volume

Plyasunov and Shock (2001) – 2 acetic acid, propanoic acid, and methane

  • DEW model (2017) – 1 methane: revised with new predicted a1 for complex species

Facq et al. (2014) – 3 CO2, CO3-2, and HCO3-

Sverjensky et al. (2014) – 2 SiO2 and Si2O4

DEW model (2017) – 184 other data from Aqueous Species Table in spreadsheet (see detailed references there)

  • DEW model (2017) – 1 acetate: revised January 26th, 2016; new a1 value from complexes and organics correlation.

  • DEW model (2017) – 1 MgCl+: revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions

  • DEW model (2017) – 1 NaCl: revised with new predicted a1 for complex species

SUPCRT92 (180)

These minerals and aqueous species, taken from the SUPCRT92 database, were present in earlier versions of CHNOSZ but have since been superseded by Berman (1988) (minerals) and Nordstrom and Archer (2003) (H2AsO3-). The thermodynamic properties and parameters are kept here as optional data for reproducing published calculations and making comparisons with newer data. The minerals here include all of the silicates and Al-bearing minerals from Helgeson et al. (1978), as well as calcite, dolomite, hematite, and magnetite. Use add.obigt("SUPCRT92") to load the data. NOTE: Other minerals from SUPCRT92, including native elements, sulfides, halides, sulfates, and selected carbonates and oxides that do not duplicate those in the Berman dataset, are still present in the default database (inorganic_cr.csv).

Helgeson et al. (1978) – 178 data for minerals and phase transitions (ø)

  • Kelley (1960) – 1 larnite Cp (ø)

  • Robie et al. (1978) – 4 dickite, fluorphlogopite, halloysite, and pyrope (ø)

  • Plummer and Busenberg (1982) – 2 aragonite and calcite (ø)

  • Helgeson (1985) – 1 ferrosilite and siderite (ø)

  • sprons92.dat – 24 Ca-bearing minerals; “Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca2+ and CO32- (Shock and Helgeson, 1988) together with the solubilities of calcite and aragonite reported by Plummer and Busenberg (1982) (ø)

  • slop98.dat – 1 daphnite; “Gf and Hf from Saccocia and Seyfried (1993) TMM” (*)

  • CHNOSZ – 53 GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.

Robie et al. (1978) – 2 rutile and titanite (ø)

  • Bowers and Helgeson (1983) – 1 rutile (ø)

  • sprons92.dat – 1 titanite: Bowers and Helgeson (1983) + “Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca2+ and CO32- (Shock and Helgeson, 1988) together with the solubilities of calcite and aragonite reported by Plummer and Busenberg (1982) (ø)

SLOP98 (169)

These species, which were taken from or are linked to slop98.dat (or later versions) and were present in earlier versions of CHNOSZ, have been replaced by or are incompatible with species currently in the default database, including aqueous Al species (Tagirov and Schott, 2001), As species (Nordstrom and Archer, 2003), Au, Ag, and Cu species (Akinfiev and Zotov, 2001; Akinfiev and Zotov, 2010), Pd species (Tagirov et al., 2013), Zn species (Akinfiev and Tagirov, 2014), and Pt species (Tagirov et al., 2015). This file also contains aqueous transuranic actinide complexes, for which estimated thermodynamic properties have been reported, but no entropies of the corresponding elements at 298.15 K are available to check the self-consistency of the GHS values for the complexes. Use add.obigt("SLOP98") to load the data. NOTE: Many other species found in slop98.dat and later versions are still present in the default database.

Shock and Helgeson (1988) – 1 H2AsO3- (ø)

Shock and Helgeson (1988) – 1 Ag+ (ø)

Shock and Koretsky (1993) – 9 Ag-, Au-, Cu(I)- and Al-acetate complexes (*)

McCollom and Shock (1997) – 1 aqueous HCl (*)

  • slop98.dat – 1 “Data and parameters as used by McCollom and Shock (1997).” (*)

Shock et al. (1997) – 1 aqueous ions and hydroxide complexes (*)

Shock et al. (1997) – 2 Au+ and Cu+ (*)

  • Shock and Helgeson (1988) – 2 values of GHS

Shock et al. (1997) – 6 arsenate and arsenite species (*)

Shock et al. (1997) – 5 Al+3 and Al-hydroxide complexes (*)

Shock et al. (1997) – 5 Zn+2 and Zn-hydroxide complexes (*)

  • Shock and Helgeson (1988) – 1 values of GHS

Sverjensky et al. (1997) – 2 Au(HS)2- and Ag(HS)2- (*)

Sverjensky et al. (1997) – 10 Au-, Ag-, Cu- and Zn-chloride complexes (*)

Sverjensky et al. (1997) – 3 Zn-acetate complexes (*)

  • slop16.dat – 1 Zn(Ac)3-: “Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote h in table 2 of Sverjensky et al. (1997).” (‡)

Sassani and Shock (1998) – 20 Pd+2 and Pt+2 and their complexes (*)

Murphy and Shock (1999) – 38 actinides (†)

Prapaipong et al. (1999) – 9 metal-dicarboxylate complexes (†)

  • slop07.dat – 1 corrected charge of Pu(Oxal)+2 (†)

  • CHNOSZ – 2 charge of NpO2(Oxal), La(Succ)+, NH4(Succ)-, and NpO2(Succ) as listed by Prapaipong et al. (1999)

Prapaipong et al. (1999) – 2 Al(Mal)+ and Al(Oxal)+ (†)

Marini and Accornero (2007) – 52 metal-arsenate and metal-arsenite complexes; linked to properties of arsenate and arsenite from Shock et al. (1997)

  • Marini and Accornero (2010) – 52 corrected values

Accornero et al. (2010) – 2 Np- and Am-chromate complexes

OldAA (64)

Data for these amino acids and related species were present in earlier versions of CHNOSZ but have been replaced by or are incompatible with later updates (LaRowe and Dick, 2012; Kitadai, 2014; Azadi et al., 2019). Use add.obigt("OldAA") to load the data.

Shock (1992) – 4 diglycine, alanylglycine, leucylglycine, and diketopiperazine; not present in slop files after slop98.dat (*)

Shock and Koretsky (1995) – 54 alanate, glycinate and their complexes with metals. Values are taken from slop98.dat, which notes corrected values for some species. (*)

  • Amend and Helgeson (1997) – 2 alanate and glycinate GHS

  • CHNOSZ – 52 metal-amino acid complexes: GHS were recalculated by adding the differences between values from Shock and Koretsky (1995) and Amend and Helgeson (1997) for alanate or glycinate to the properties of the complexes reported by Shock and Koretsky (1995).

Amend and Helgeson (1997) – 3 glycine, glycinium, and methionine GHS

  • Dick et al. (2006) – 3 amino acids HKF parameters

Dick et al. (2006) – 3 [Gly], [Met], and [UPBB]

AS04 (3)

This file has data for aqueous SiO2 from Apps and Spycher (2004) and a modified HSiO3- to be consistent with the SiO2 here. This file also has H4SiO4 from an earlier publication (Stefánsson, 2001) that is roughly consistent with SiO2 here (see ?add.obigt). Use add.obigt("AS04") to load the data; see Regressing thermodynamic data for an example.

Sverjensky et al. (1997) – 1 HSiO3- (*)

  • CHNOSZ – 1 GHS recalculated by adding difference from SiO2 (Sverjensky et al., 1997) to updated values for SiO2 (Apps and Spycher, 2004)

Stefánsson (2001) – 1 aqueous H4SiO4

Apps and Spycher (2004) – 1 aqueous SiO2

AkDi (24)

This file has parameters for aqueous nonelectrolytes in the Akinfiev-Diamond model (Akinfiev and Diamond, 2003). Use add.obigt("AkDi") to load the data; see demo(AkDi) for an example.

Akinfiev and Diamond (2003) – 10 dissolved gas species; parameters estimated from the experimental Henry’s constant

Akinfiev and Diamond (2003) – 8 dissolved gas species; parameters estimated from standard-state properties at 25 ° C

Akinfiev and Plyasunov (2014) – 6 B(OH)3, Si(OH)4, and As(OH)3

Total count of species

3372 of 3372 entries in thermo()$obigt and 639 optional data entries are documented here.

References

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Richard L, Helgeson HC. 1998. Calculation of the thermodynamic properties at elevated temperatures and pressures of saturated and aromatic high molecular weight solid and liquid hydrocarbons in kerogen, bitumen, petroleum, and other organic matter of biogeochemical interest. Geochimica et Cosmochimica Acta 62(23-24): 3591–3636. doi: 10.1016/S0016-7037(97)00345-1

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Saccocia PJ, Seyfried WE. 1993. A resolution of discrepant thermodynamic properties for chamosite retrieved from experimental and empirical techniques. American Mineralogist 78(5-6): 607–611. Available at http://ammin.geoscienceworld.org/content/78/5-6/607.

Sassani DC, Shock EL. 1998. Solubility and transport of platinum-group elements in supercritical fluids: Summary and estimates of thermodynamic properties for ruthenium, rhodium, palladium, and platinum solids, aqueous ions, and complexes to 1000°C and 5 kbar. Geochimica et Cosmochimica Acta 62(15): 2643–2671. doi: 10.1016/S0016-7037(98)00049-0

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Schulte MD, Shock EL. 1993. Aldehydes in hydrothermal solution: Standard partial molal thermodynamic properties and relative stabilities at high temperatures and pressures. Geochimica et Cosmochimica Acta 57(16): 3835–3846. doi: 10.1016/0016-7037(93)90337-V

Schulte MD, Shock EL, Wood RH. 2001. The temperature dependence of the standard-state thermodynamic properties of aqueous nonelectrolytes. Geochimica et Cosmochimica Acta 65(21): 3919–3930. doi: 10.1016/S0016-7037(01)00717-7

Shock EL. 1992. Stability of peptides in high-temperature aqueous solutions. Geochimica et Cosmochimica Acta 56(9): 3481–3491. doi: 10.1016/0016-7037(92)90392-V

Shock EL. 1993. Hydrothermal dehydration of aqueous organic compounds. Geochimica et Cosmochimica Acta 57(14): 3341–3349. doi: 10.1016/0016-7037(93)90542-5

Shock EL. 1995. Organic acids in hydrothermal solutions: Standard molal thermodynamic properties of carboxylic acids and estimates of dissociation constants at high temperatures and pressures. American Journal of Science 295(5): 496–580. doi: 10.2475/ajs.295.5.496

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Shock EL, Helgeson HC. 1990. Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: Standard partial molal properties of organic species. Geochimica et Cosmochimica Acta 54(4): 915–945. doi: 10.1016/0016-7037(90)90429-O

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Shock EL, Koretsky CM. 1993. Metal-organic complexes in geochemical processes: Calculation of standard partial molal thermodynamic properties of aqueous acetate complexes at high pressures and temperatures. Geochimica et Cosmochimica Acta 57(20): 4899–4922. doi: 10.1016/0016-7037(93)90128-J

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